Changes In Microbial Function Research Articles

Here to stay. Recent advances and perspectives about Acacia invasion in Mediterranean areas

• Key message The above- and belowground impacts due to Acacia invasions have been described in detail over the last 25 years. Future research should focus on the early detection and prevention of new Acacia introductions and on a cost-effective and sustainable management of the novel ecosystems resulting from invasions. • Context Invasive alien plants (IAPs) strongly alter ecosystems reducing biodiversity, modifying ecosystem services and increasing negative impacts at social and economic level. Among invasive taxa, Acacia is a highly problematic genus worldwide. In fact, almost 500 papers have been published on several aspects of Acacia invasions for the last 25 years. • Aims We aim at reviewing the current knowledge on the consequences of the invasion by Acacia genus in Mediterranean ecosystems. We also collect and propose different approaches for the management and recovery of invaded areas and suggest future perspectives on Acacia research. • Methods We compile, summarise and discuss recent findings on physicochemical, ecological, microbiological and socioeconomic aspects of invasion related to Australian acacias (Acacia dealbata, Acacia longifolia, Acacia mearnsii, Acacia saligna and Acacia melanoxylon) focusing on Mediterranean areas. • Results Acacia invasion generally entails soil physicochemical alterations and changes in microbial function and structure. Consequences such as the decreased biodiversity, altered ecosystem structure, larger seed banks dominated by invasive species, new biotrophic relationships or alterations in water availability and fire regimes suggest that acacias are locally creating novel ecosystems. • Conclusions Forecasting invasions, modelling and managing ecosystems dominated by acacias are challenging tasks that should be addressed in the future, since climatic conditions and intensification in land uses are increasing the likelihood of Acacia invasions in Mediterranean areas. Unsuccessful management actions suggest that restoration should be meticulously monitored, but the magnitude of invasion or the inconsistency of economic investment indicate that eradication is often unfeasible. Alternatively, novel integrative and cost-effective solutions including the collaboration of society, politicians and stakeholders are necessary to prevent new introductions and achieve sustainable control of acacias. There is a growing interest in applied research on the valorisation or novel uses for acacias and their residues that result in economic benefits.

Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues

Decomposition of organic matter is crucial for ecosystem functioning. Microorganisms, which are responsible for the mineralization of organic matter, are usually treated as a homogeneous functional guild, despite mineralization capacity can differ profoundly between taxa. In addition, a significant part of the microbial community is top-down controlled by microbial grazers, such as protist. Since protist grazing is selective, and selectivity differs among species, we hypothesized that protist taxa complement each other in grazing intensity and thereby affect bacterial community structure and mineralization rate. In a laboratory experiment the species richness of protist communities was manipulated in an arable field soil and the mineralization rate of maize litter residues followed during the decomposition of the labile (4 days) and recalcitrant (3 weeks) carbon (C) fractions. Mineralization rate overall increased in the presence of protists. Changes in microbial function could be related to changes in microbial community composition (measured by phospholipid fatty acids pattern). During microbial decomposition, different protist grazers gained influence on mineralization rates over consecutive time intervals, indicating that a succession of protists caused an enhanced bacterial C-mineralization of plant detritus. Protist identity and species richness affected the microbial community composition, but not the magnitude of its mineralization function. In general, protist identity appeared to be more relevant for the composition of the microbial communities at the beginning of decomposition while the protist species richness appeared to be more critical in the later, slow phase of decomposition. This study provides an example that the overall outcome of ecosystem processes, such as mineralization rate is regulated by the sum of positive and negative effects of complex species interactions operating at a very fine spatial and temporal scales.

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition.

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.

Warming and elevated CO2 combine to increase microbial mineralisation of soil organic matter

The net annual exchange of carbon between the atmosphere and terrestrial ecosystems is of prime importance in determining the concentration of CO2 ([CO2]) in the atmosphere and consequently future climate. Carbon loss occurs primarily through soil respiration; it is known that respiration is sensitive to the global changes in [CO2] and temperature, suggesting that the net carbon balance may change in the future. However, field manipulations of temperature and [CO2] alter many important environmental factors so it is unclear how much of the observed alterations in soil respiration is due to changes of microbial function itself instead of changes to the physical and chemical environment. Here we focus on resolving the importance of changes in the microbial community in response to warming and elevated [CO2] on carbon mineralisation, something not possible in field measurements. We took plant material and soil inocula from a long running experiment where native grassland had been exposed to both warming and elevated CO2 and constructed a reciprocal transplant experiment. We found that the rate of decomposition (heterotrophic respiration) was strongly determined by the origin of the microbial community. The combined warming + elevated CO2 treatment produced a soil community that gave respiration rates 30% higher when provided with shoot litter and 70% for root litter than elevated CO2 treatment alone, with the treatment source of the litter being unimportant. Warming, especially in the presence of elevated CO2, increased the size of the apparent labile carbon pool when either C3 or C4 litter was added. Thus, the metabolic activity of the soil community was affected by the combination of warming and elevated CO2 such that it had an increased ability to mineralise added organic matter, regardless of its source. Therefore, soil C efflux may be substantially increased in a warmer, high CO2 world. Current ecosystem models mostly drive heterotrophic respiration from plant litter quality, soil moisture and temperature but our findings suggest equal attention will need to be paid to capturing microbial processes if we are to accurately project the future C balance of terrestrial ecosystems and quantify the feedback effect on atmospheric concentrations of CO2.

Dynamics of gut microbiota in autoimmune lupus.

Gut microbiota has been recognized as an important environmental factor in health, as well as in metabolic and immunological diseases, in which perturbation of the host gut microbiota is often observed in the diseased state. However, little is known on the role of gut microbiota in systemic lupus erythematosus. We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model. In young, female lupus-prone mice resembling women at childbearing age, a population with the highest risk for lupus, we found marked depletion of lactobacilli, and increases in Lachnospiraceae and overall diversity compared to age-matched healthy controls. The predicted metagenomic profile in lupus-prone mice showed a significant enrichment of bacterial motility- and sporulation-related pathways. Retinoic acid as a dietary intervention restored lactobacilli that were downregulated in lupus-prone mice, and this correlated with improved symptoms. The predicted metagenomes also showed that retinoic acid reversed many lupus-associated changes in microbial functions that deviated from the control. In addition, gut microbiota of lupus-prone mice were different between sexes, and an overrepresentation of Lachnospiraceae in females was associated with an earlier onset of and/or more severe lupus symptoms. Clostridiaceae and Lachnospiraceae, both harboring butyrate-producing genera, were more abundant in the gut of lupus-prone mice at specific time points during lupus progression. Together, our results demonstrate the dynamics of gut microbiota in murine lupus and provide evidence to suggest the use of probiotic lactobacilli and retinoic acid as dietary supplements to relieve inflammatory flares in lupus patients.

Exposure of mice to high fat diet shifts gut microbiota community structure and alters microbial function in a diurnal manner (637.17)

Many organisms exhibit circadian rhythms (CC) based on a 24‐hour light/dark cycle. Evidence in mammalian systems highlights the dominant role of CC in maintaining health, in that development of diet‐induced obesity is associated with CC disruption. Studies also show that high fat (HF) diet‐induced gut microbiota contributes to the development of obesity. Whether the gut microbiota exhibits its own diurnal patterns under healthy states that becomes perturbed under conditions of HF feeding has yet to be described. We hypothesized that HF diet‐induced gut microbiota exhibit altered structural and functional diurnal patterns that ultimately influence host metabolism. Thirty‐six individually‐housed adult C57/Bl6J male mice maintained on a 12/12 light:dark cycle were fed regular chow (RC) or HF diet for 5 weeks. Three mice per treatment were harvested over 24hrs at six time points. Assessment of cecal bacterial 16s rRNA V4‐V5 region via Illumina MiSeq showed MF diet resulted in significantly different α and β‐diversity community structure compared to RC. Diurnal variations in 16s structure were evident in both RC and HF communities, although significant differences over time were not achieved in either treatment. However, comparison of RC and HF cecal microbial community functional profiles via inoculation into Biolog GenIII plates (a spectrophotometric assessment of carbon‐based cellular respiration) showed that while RC and HF exhibited significantly different metabolic potential, only HF exhibited significant diurnal patterns. Together, the data suggest that HF diet alters community membership and only differences in diurnal community functional properties are exhibited. The role of the HF diet‐induced microbial functional changes on the development of obesity in the host remains to be elucidated.Grant Funding Source: Supported By NIDDK P30DK42086

Microbial function in adjacent subtropical forest and agricultural soil

Soil microbial communities and their activities are altered by land use change; however impacts and extent of these alterations are often unclear. We investigated the functional responses of soil microbes in agricultural soil under sugarcane and corresponding native soil under Eucalyptus forest to additions of contrasting plant litter derived from soybean, sugarcane and Eucalyptus in a microcosm system, using a suite of complimentary techniques including enzyme assays and community level physiological profiles (CLPP). Initially agricultural soil had 50% less microbial biomass and lower enzyme activities than forest soil, but significantly higher nitrification rates. In response to litter addition, microbial biomass increased up to 11-fold in agricultural soil, but only 1.8-fold in forest soil, suggesting a prevalence of rapidly proliferating ‘r’ and slower growing ‘K’ strategists in the respective soils. Litter-driven change in microbial biomass and activities were short lived, largely returning to pre-litter addition levels by day 150. Decomposition rates of sugarcane and soybean litter as estimated via CO2 production were lower in agricultural than in forest soil, but decomposition of more recalcitrant Eucalyptus litter was similar in both soils, contradicting the notion that microbial communities specialise in decomposing litter of the dominant local plant species. Enzyme activities and community level physiological profiles (CLPP) were closely correlated to microbial biomass and overall CO2 production in the agricultural soil but not the forest soil, suggesting contrasting relationships between microbial population dynamics and activity in the two soils. Activities of enzymes that break down complex biopolymers, such as protease, cellulase and phenol oxidase were similar or higher in the agricultural soil, which suggests that the production of extracellular biopolymer-degrading enzymes was not a factor limiting litter decomposition. Enzyme and CLPP analyses produced contrasting profiles of microbial activity in the two soils; however the combination of both analyses offers additional insights into the changes in microbial function and community dynamics that occur after conversion of forest to agricultural land.

Characterizing the relationships between soil organic matter components and microbial function and composition along a tillage disturbance gradient

We studied the effect of no-till (disc seeder), conventional-till (tine scarifier+disc seeder) and rotary-till (rotary hoe+disc seeder) management on soil organic matter (SOM) components, rates of carbon (C) and nitrogen (N) cycling, substrate utilization and microbial community composition. We hypothesized that labile SOM fractions are sensitive to changes in tillage techniques and, in turn mediate any tillage-induced changes in microbial function and composition. A replicated field site was established in May 1998 in the semi-arid agricultural region of Western Australia and soils were collected in September 2004. We found soil pH varied between different tillage techniques as an initial lime application was mixed to deeper soil depths in rotary-till soil than no-till and conventional-till soil. Total-C was greater in surface soil and lower in subsurface soil from no-till and conventional-till plots than from rotary-till plots, but there was no effect of tillage technique on total-C when averaged across soil depths. Light (specific density <1.0 g cm −3) fraction organic matter (LFOM), dissolved organic matter (DOM) and microbial biomass (MB) C and N pools, and rates of C and N cycling all tended to decrease with soil depth. In general, LFOM-C and N, dissolved organic C (DOC) and microbial biomass carbon (MB-C), soil respiration, cellulase activity, gross immobilization rates were positively correlated ( r>0.50) and were greater in no-till and conventional-till soil than rotary-till soil both within, and across soil depths. These soil variables generally increased ( r>0.5) with increasing soil pH. Dissolved organic N and gross N mineralization were positively correlated ( r>0.90) but neither was affected by tillage techniques. No-till soil had greater utilization of carboxylic acids and lower utilization of amino acids and carbohydrates than conventional-till and rotary-till soil; surface soil also had greater utilization of carboxylic acids than subsurface soil. In turn, substrate utilization differed between soil depths, and between no-till soil and conventional-till and rotary-till soil; these differences were correlated with soil pH, total-N, DOC, LFOM-N and microbial biomass nitrogen (MB-N). Bacterial and fungal biomasses generally decreased with soil depth and were greater in no-till and conventional-till soil than rotary-till soil. Microbial community composition differed between all tillage techniques and soil depths; these differences were correlated with soil textural classes, soil pH, and total, LFOM, DOM and microbial C and N pools. These results indicate that most tillage-induced changes to soil properties were associated with the greater soil disturbance under rotary-till than under no-till or conventional-till management. Our results indicate that tillage-induced changes to soil pH, and LFOM, DOM and microbial biomass pools are likely to be important regulators of the rates of C and N cycling, substrate utilization and microbial community composition in this coarse textured soil.

Seasonal changes in microbial function and diversity associated with stubble retention versus burning

The long-term (16-year) effect of stubble management (i.e. retained or burnt) on the size of the microbial community (microbial biomass-C and -N), microbial community structure (PLFA), and function (CO2-C evolution, gross N transformation rates, enzymatic activity, and community level physiological profiles) was investigated on 4 occasions during a single wheat-growing season using soil collected from the low-rainfall (&lt;250 mm) region of Western Australia. Significant differences (P &lt; 0.001) in microbial community structure and function were determined for different sampling times by phospholipid fatty acid (PLFA) analyses and community level physiological profiles (CLPP). However, neither PLFA nor CLPP analyses identified differences between stubble treatments. In contrast to total soil organic matter-C, for which no treatment differences were evident, microbial biomass-C was 34% and CO2-C evolution 61% greater in stubble-retained treatments than in burnt-stubble treatments in the 0–0.05 m soil layer. Seasonal increases in microbial biomass-C (P &lt; 0.001) were on average twice as large and CO2-C evolution (P &lt; 0.001) nearly 4 times greater in September during crop flowering compared with other sampling times. In contrast, microbial biomass-N remained constant throughout the entire sampling period. Stubble-retained treatments also demonstrated significantly greater (P &lt; 0.05) levels of arginine ammonification, acid phosphatase and β-glucosidase enzyme activity on average compared with burnt-stubble treatments. However, the effect (P = 0.05) of stubble treatment on gross N mineralisation, nitrification, or immobilisation rates was seasonally dependent with burnt-stubble treatments demonstrating lower gross N mineralisation rates than retained-stubble treatments in November. Gross N mineralisation was lower (37–83% on average) than potential gross nitrification rates (estimated in the presence of excess NH4+) measured from May to September. The rate of potential gross nitrification was observed to decline significantly (P = 0.06) in November and as a result, more closely matched gross N mineralisation rates. Potential gross nitrification rates were also up to 6 times greater than microbial immobilisation of NH4+, indicating that this would be the primary consumptive process in the presence of NH4+. Whilst potential nitrification rates in the presence of excess NH4+ were high, low soil NO3– concentrations indicate that plant/microbial demand for NO3– and NH4+ exceeded the supply capacity. For example, actual gross nitrification rates (determined in the presence of 15N-labelled NO3-) were only greater than gross N mineralisation in May, indicating N supply constrained nitrification at other sampling times. Findings illustrate that increased wheat yields of 31% in this study were associated with the retention of stubble. Further they demonstrate that changes in stubble management significantly influenced the mass and activity of microorganisms (and in some cases N cycling), whilst having little influence on community diversity.

Impact of genetically modified crops and their management on soil microbially mediated plant nutrient transformations.

One of the potential environmental effects of the recent rapid increase in the global agricultural area cultivated with transgenic crops is a change in soil microbially mediated processes and functions. Among the many essential functions of soil biota are soil organic matter decomposition, nutrient mineralization and immobilization, oxidation-reduction reactions, biological N fixation, and solubilization. However, relatively little research has examined the direct and indirect effects of transgenic crops and their management on microbially mediated nutrient transformations in soils. The objectives of this paper are to review the available literature related to the environmental effects of transgenic crops and their management on soil microbially mediated nutrient transformations, and to consider soil properties and climatic factors that may affect the impact of transgenic crops on these processes. Targeted genetic traits for improved plant nutrition include greater plant tolerance to low Fe availability in alkaline soils, enhanced acquisition of soil inorganic and organic P, and increased assimilation of soil N. Among the potential direct effects of transgenic crops and their management are changes in soil microbial activity due to differences in the amount and composition of root exudates, changes in microbial functions resulting from gene transfer from the transgenic crop, and alteration in microbial populations because of the effects of management practices for transgenic crops, such as pesticide applications, tillage, and application of inorganic and organic fertilizer sources. Possible indirect effects of transgenic crops, including changes in the fate of transgenic crop residues and alterations in land use and rates of soil erosion, deserve further study. Despite widespread public concern, no conclusive evidence has yet been presented that currently released transgenic crops, including both herbicide and pest resistant crops, are causing significant direct effects on stimulating or suppressing soil nutrient transformations in field environments. Further consideration of the effects of a wide range of soil properties, including the amount of clay and its mineralogy, pH, soil structure, and soil organic matter, and variations in climatic conditions, under which transgenic crops may be grown, is needed in evaluating the impact of transgenic crops on soil nutrient transformations. Future environmental evaluation of the impact of the diverse transgenic crops under development could lead to an improved understanding of soil biological functions and processes.

A prototype system for resource allocation related to the actual disability and comorbidity of patients

There have been numerous human studies reporting associations between the intestinal microbiome and functional gastrointestinal disorders (FGIDs), and independently animal studies have explored microbiome-driven mechanisms underlying FGIDs. However, there is often a disconnect between human and animal studies, which hampers translation of microbiome findings to the clinic. Changes in the microbiota composition of patients with FGIDs are generally subtle, whereas changes in microbial function, reflected in the fecal metabolome, appear to be more precise indicators of disease subtype-specific mechanisms. Although we have made significant progress in characterizing the microbiome, to effectively translate microbiome science in a timely manner, we need concurrent and iterative longitudinal studies in humans and animals to determine the precise microbial functions that can be targeted to address specific pathophysiological processes in FGIDs. A systems approach integrating multiple data layers rather than evaluating individual data layers of symptoms, physiological changes, or -omics data in isolation will allow for validation of mechanistic insights from animal studies while also allowing new discovery. Patient stratification for clinical trials based on functional microbiome alterations and/or pathophysiological measurements may allow for more accurate determination of efficacy of individual microbiome-targeted interventions designed to correct an underlying abnormality. In this review, we outline current approaches and knowledge, and identify gaps, to provide a potential roadmap for accelerating translation of microbiome science toward microbiome-targeted personalized treatments for FGIDs.

Nitrogen Mineralization and Nitrification in Suburban and Undeveloped Atlantic White Cedar Wetlands

AbstractThe presence of urban and suburban lands adjacent to wetlands may cause changes in nutrient‐cycling processes, due to changes in the quality of the ground‐ and surface waters that drain from the developed uplands into the wetland. We studied N‐cycling processes in Atlantic white cedar [Chamaecyparis thyoides (L.)] swamps in the New Jersey Pinelands to determine their sensitivity to the development of adjoining uplands. We conducted a 19‐wk aerobic incubation to measure N mineralization and nitrification potentials in wetland soils from both developed and undeveloped watersheds. The cumulative inorganic N mineralized during the incubation was two to three times higher in soils from developed sites than from the undeveloped sites. There was virtually no nitrification in undeveloped wetlands, while in developed wetlands, most N mineralized was further nitrified. In developed sites, there was also more nitrification in hollow soils than in hummock soils. Both nitrification and the fraction of soil organic matter mineralized were highly correlated with pH and with soil ash content. These results suggest that increases in ash content of peats attributable to sediment transported and deposited in urban runoff, causes increases in pH, which in turn allows large populations of nitrifiers to develop. Excess mineral N generated within the wetlands through changes in microbial function thus may be as important as N inputs in drainage water in affecting plant community composition, and may cause wetlands to become sources of N to downstream ecosystems rather than serving as regional sinks.